After installing 3 LDAP files-sets in IBM AIX 7 and rebooting the system using the
(# shutdown -Fr) commands, I can't a gain connect to this server via PUTTY; whatever the port was (ssh / telnet / ftp)
With HMC the connection is still possible.

Yes this package is present, but we are not allowed to remove it.
The client I use is a windows SEVEN client, I don't know how to first
check the ssh keys between this client and server before suggesting to my
team to remove the package.

You might try another terminal client program, like securecrt, but not sure if it will work, we have to remove that package in order windows machines can connect back, on linux clients me an other sysadmin didn't have any problem